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- PDB-2p9k: Crystal structure of bovine Arp2/3 complex co-crystallized with A... -

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Basic information

Entry
Database: PDB / ID: 2p9k
TitleCrystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with glutaraldehyde
Components
  • (Actin-like protein ...) x 2
  • (Actin-related protein 2/3 complex subunit ...) x 5
KeywordsSTRUCTURAL PROTEIN / complex / actin / WD repeat
Function / homology
Function and homology information


muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of actin filament polymerization ...muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of actin filament polymerization / cilium assembly / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / cell projection / structural constituent of cytoskeleton / actin filament binding / synaptic vesicle membrane / cell migration / lamellipodium / site of double-strand break / actin binding / cell cortex / postsynapse / neuron projection / endosome / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Yope Regulator; Chain: A, / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 ...Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Yope Regulator; Chain: A, - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Yope Regulator; Chain: A, / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / ATPase, nucleotide binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Nucleotidyltransferase; domain 5 / Alpha Horseshoe / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin-related protein 2 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsNolen, B.J. / Pollard, T.D.
CitationJournal: Mol.Cell / Year: 2007
Title: Insights into the Influence of Nucleotides on Actin Family Proteins from Seven Structures of Arp2/3 Complex.
Authors: Nolen, B.J. / Pollard, T.D.
History
DepositionMar 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-like protein 3
B: Actin-like protein 2
C: Actin-related protein 2/3 complex subunit 1B
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,34111
Polymers224,2477
Non-polymers1,0954
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21880 Å2
ΔGint-121 kcal/mol
Surface area71150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.620, 128.050, 198.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Actin-like protein ... , 2 types, 2 molecules AB

#1: Protein Actin-like protein 3 / Actin-related protein 3


Mass: 47428.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ACTR3 / References: UniProt: P61157
#2: Protein Actin-like protein 2 / Actin-related protein 2


Mass: 44834.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ACTR2 / References: UniProt: A7MB62

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Actin-related protein 2/3 complex subunit ... , 5 types, 5 molecules CDEFG

#3: Protein Actin-related protein 2/3 complex subunit 1B / ARP2/3 complex 41 kDa subunit / p41-ARC


Mass: 41016.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARPC1B / References: UniProt: Q58CQ2
#4: Protein Actin-related protein 2/3 complex subunit 2 / ARP2/3 complex 34 kDa subunit / p34-ARC


Mass: 34402.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARPC2 / References: UniProt: Q3MHR7
#5: Protein Actin-related protein 2/3 complex subunit 3 / ARP2/3 complex 21 kDa subunit / p21-ARC


Mass: 20572.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARPC3 / References: UniProt: Q3T035
#6: Protein Actin-related protein 2/3 complex subunit 4 / ARP2/3 complex 20 kDa subunit / p20-ARC


Mass: 19697.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARPC4 / References: UniProt: Q148J6
#7: Protein Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit / p16-ARC


Mass: 16295.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARPC5 / References: UniProt: Q3SYX9

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Non-polymers , 3 types, 400 molecules

#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7.5% PEG 3350, 50mM HEPES, 100mM KSCN, 10% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. all: 89458 / Num. obs: 88027 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.099 / Χ2: 1.472 / Net I/σ(I): 11.2
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.03 / Num. unique all: 7621 / Χ2: 1.694 / % possible all: 86.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4286 4.9 %RANDOM
Rwork0.219 ---
all0.222 89458 --
obs0.222 84915 96.3 %-
Solvent computationBsol: 21.309 Å2
Displacement parametersBiso mean: 35.609 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2---4.051 Å20 Å2
3---7.851 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13902 0 64 396 14362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3391.5
X-RAY DIFFRACTIONc_scbond_it2.0042
X-RAY DIFFRACTIONc_mcangle_it2.2942
X-RAY DIFFRACTIONc_scangle_it3.0372.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3atp.param
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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